New amino acid substitution matrix brings sequence alignments into agreement with structure matches.

ABSTRACT: Protein sequence matching presently fails to identify many structures that are highly similar, even when they are known to have the same function. The high packing densities in globular proteins lead to interdependent substitutions, which have not previously been considered for amino acid similarities. At present, sequence matching compares sequences based only upon the similarities of single amino acids, ignoring the fact that in densely packed protein, there are additional conservative substitutions representing exchanges between two interacting amino acids, such as a small-large pair changing to a large-small pair substitutions that are not individually so conservative. Here we show that including information for such pairs of substitutions yields improved sequence matches, and that the

SUBMITTER: Jia K 

PROVIDER: S-EPMC8641535 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature